Last updated: 2019-01-04
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The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
✖ Environment: objects present
wflow_publish or wflow_build to ensure that the code is always run in an empty environment. The following objects were defined in the global environment when these results were created:
| Name | Class | Size |
|---|---|---|
| alignMerge | cwlStepParam | 301.6 Kb |
| fq1 | list | 832 bytes |
| fq2 | list | 832 bytes |
| inputList | list | 3.5 Kb |
| mc3 | cwlStepParam | 90.6 Kb |
| paramList | list | 576 bytes |
| rgs | list | 880 bytes |
| samples | list | 592 bytes |
✔ Seed:
set.seed(20181205)
The command set.seed(20181205) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded
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✔ Repository version: e8464d6
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Untracked files:
Untracked: analysis/Rcwl_DNASeq_Align.Rmd
Untracked: analysis/Rcwl_DNASeq_Align.Rmd~
Untracked: analysis/Rcwl_GATK4.Rmd
Untracked: analysis/Rcwl_GATK4.Rmd~
Untracked: analysis/Rcwl_MC3.Rmd
Untracked: analysis/Rcwl_MC3.Rmd~
Untracked: bwaOutput.sam
Untracked: code/gatk.R
Untracked: code/gatk.R~
Untracked: data/fq1_1.fq
Untracked: data/fq1_2.fq
Untracked: data/fq2_1.fq
Untracked: data/fq2_2.fq
Untracked: data/normal.bam
Untracked: data/normal.bam.bai
Untracked: data/normal_1.fq
Untracked: data/normal_2.fq
Untracked: data/tumor.bam
Untracked: data/tumor.bam.bai
Untracked: data/tumor_1.fq
Untracked: data/tumor_2.fq
Untracked: file571cd084c44/
Untracked: output/BAM/
Untracked: output/GATK/
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Untracked: output/interval.21.intervals
Untracked: output/interval.list~
Untracked: output/interval.txt
Untracked: output/mc3/
Untracked: sample1.bam
Untracked: sample1.bam.bai
Untracked: tmpl1.json
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The DNASeq alignment pipeline was included in the RcwlPipelines package. It majorly includes two steps:
Here is the short summary and step plots.
suppressPackageStartupMessages(library(Rcwl))
library(RcwlPipelines)
data("alignMerge")
short(alignMerge)
inputs:
- idBam
- RG
- threads
- Ref
- FQ1s
- FQ2s
outputs:
- oBam
- matrix
- Idx
- stat
steps:
- bwaAlign
- mergeBamDup
plotCWL(alignMerge)
plotCWL(runs(alignMerge)$bwaAlign)
plotCWL(runs(alignMerge)$mergeBamDup)
Here is an example of two samples. The “sample1” have two lanes of sequences and the “sample2” only has one pair of reads. The lists of reads1 fq1, reads2 fq2, read groups and output BAM names are defined in the inputList. The reference genome and number of threads to run the job are defined in the shared options, paramList.
fq1 <- list(sample1 = list("data/fq1_1.fq", "data/fq2_1.fq"),
sample2 = list("data/fq1_1.fq"))
fq2 <- list(sample1 = list("data/fq1_2.fq", "data/fq2_2.fq"),
sample2 = list("data/fq1_2.fq"))
rgs <- list(sample1 = list("@RG\\tID:sample1.1\\tSM:sample1", "@RG\\tID:sample1.2\\tSM:sample1"),
sample2 = list("@RG\\tID:sample2.1\\tSM:sample2"))
samples <- list(sample1 = "sample1.bam", sample2 = "sample2.bam")
inputList <- list(idBam = samples, RG= rgs, FQ1s = fq1, FQ2s = fq2)
paramList <- list(threads = 2,
Ref = "/rpcc/bioinformatics/reference/current/hs37d5.fa")
res <- runCWLBatch(alignMerge, wdir = "output/BAM",
inputList = inputList, paramList = paramList,
BPPARAM = BatchtoolsParam(workers = 2, cluster = "sge",
template = "/rpcc/bioinformatics/sge.tmpl",
resources = list(jobname="bwa",
threads = 2,
queue = "all.q")))
Outputs:
dir("output/BAM/sample1")
[1] "sample1.bam" "sample1.bam.bai" "sample1.flagstat.txt"
[4] "sample1.markdup.txt"
sessionInfo()
R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)
Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RcwlPipelines_0.0.0.9000 jsonlite_1.6
[3] BiocParallel_1.16.2 Rcwl_0.99.7
[5] S4Vectors_0.20.1 BiocGenerics_0.28.0
[7] yaml_2.2.0 workflowr_1.1.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 tidyr_0.8.2 visNetwork_2.0.5
[4] prettyunits_1.0.2 assertthat_0.2.0 rprojroot_1.3-2
[7] digest_0.6.18 plyr_1.8.4 R6_2.3.0
[10] backports_1.1.3 evaluate_0.12 highr_0.7
[13] ggplot2_3.1.0 pillar_1.3.1 rlang_0.3.0.1
[16] progress_1.2.0 lazyeval_0.2.1 rstudioapi_0.8
[19] data.table_1.11.8 whisker_0.3-2 R.utils_2.7.0
[22] R.oo_1.22.0 checkmate_1.8.5 rmarkdown_1.11
[25] DiagrammeR_1.0.0 downloader_0.4 readr_1.3.1
[28] stringr_1.3.1 htmlwidgets_1.3 igraph_1.2.2
[31] munsell_0.5.0 compiler_3.5.2 influenceR_0.1.0
[34] rgexf_0.15.3 xfun_0.4 pkgconfig_2.0.2
[37] htmltools_0.3.6 tidyselect_0.2.5 gridExtra_2.3
[40] tibble_1.4.2 batchtools_0.9.11 XML_3.98-1.16
[43] viridisLite_0.3.0 crayon_1.3.4 dplyr_0.7.8
[46] withr_2.1.2 R.methodsS3_1.7.1 rappdirs_0.3.1
[49] grid_3.5.2 gtable_0.2.0 git2r_0.23.0
[52] magrittr_1.5 scales_1.0.0 stringi_1.2.4
[55] debugme_1.1.0 viridis_0.5.1 bindrcpp_0.2.2
[58] brew_1.0-6 RColorBrewer_1.1-2 tools_3.5.2
[61] glue_1.3.0 purrr_0.2.5 hms_0.4.2
[64] Rook_1.1-1 colorspace_1.3-2 base64url_1.4
[67] knitr_1.21 bindr_0.1.1
This reproducible R Markdown analysis was created with workflowr 1.1.1